It is worth you considering how much airflow you might be reducing if you sit the motors down lower. It may not be an issue but worth consideration. Looking at the picture above it looks a very open ended motor.

I think i remember the arms having a couple of facelifts to strengthen them so removing a few mm from the motor mounts may not be that beneficial to it's structure although that said I've printed everything at 100% and it seems quite sturdy so probably a couple of mm off the top won't matter.

An alternative you may not have thought about is to make some spacers that simply have the motor mount shape cut into them. Glue them on top of the arms when you bolt the motors on.

I would have thought dji did a lot of work with the geometry of where the motors are in relation to the body, their height, spacing, angle, weight and other various factors needed for a nicely flying model, assumedly these have been reasonably well copied here. Dropping the motors even a few mm could effect how well it flies.